X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolParserTest.java;h=28321354c42f70b233f735d1c53578043a989852;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=fb71f016a7abaddf4daec36a35e5c27d58c418cd;hpb=a54d99a6637c6d2ea2ada774a49d496ab0b374ee;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index fb71f01..2832135 100644
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -29,19 +29,20 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.StructureParser;
 
-import java.io.IOException;
 import java.util.Vector;
 
 import org.jmol.c.STR;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import MCview.PDBfile;
+import mc_view.PDBfile;
 
 /**
  * @author jimp
@@ -49,13 +50,21 @@ import MCview.PDBfile;
  */
 public class JmolParserTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /*
    * 1GAQ has been reduced to alpha carbons only
    * 1QCF is the full PDB file including headers, HETATM etc
    */
-  String[] testFile = new String[] { "./examples/1GAQ.txt",
+  String[] testFile = new String[] { "./examples/1gaq.txt",
       "./test/jalview/ext/jmol/1xyz.pdb",
-      "./test/jalview/ext/jmol/1qcf.pdb" };
+      "./test/jalview/ext/jmol/1QCF.pdb" };
 
   //@formatter:off
   // a modified and very cut-down extract of 4UJ4
@@ -106,8 +115,7 @@ public class JmolParserTest
     for (String f : testFile)
     {
       FileLoader fl = new jalview.io.FileLoader(false);
-      AlignFrame af = fl
-              .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+      AlignFrame af = fl.LoadFileWaitTillLoaded(f, DataSourceType.FILE);
       validateSecStrRows(af.getViewport().getAlignment());
     }
   }
@@ -118,21 +126,21 @@ public class JmolParserTest
     for (String pdbStr : testFile)
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
-              AppletFormatAdapter.FILE);
-      JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE);
+              DataSourceType.FILE);
+      JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
-      assertTrue(
-              "No sequences extracted from testfile\n"
-                      + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
-                              : "(No warnings raised)"), seqs != null
-                      && seqs.size() > 0);
+      assertTrue("No sequences extracted from testfile\n"
+              + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
+                      : "(No warnings raised)"),
+              seqs != null && seqs.size() > 0);
       for (SequenceI sq : seqs)
       {
-        assertEquals("JMol didn't process " + pdbStr
-                + " to the same sequence as MCView",
-                sq.getSequenceAsString(), mcseqs.remove(0)
-                        .getSequenceAsString());
+        assertEquals(
+                "JMol didn't process " + pdbStr
+                        + " to the same sequence as MCView",
+                sq.getSequenceAsString(),
+                mcseqs.remove(0).getSequenceAsString());
         AlignmentI al = new Alignment(new SequenceI[] { sq });
         validateSecStrRows(al);
       }
@@ -167,13 +175,15 @@ public class JmolParserTest
 
   private void checkFirstAAIsAssoc(SequenceI sq)
   {
-    assertTrue("No secondary structure assigned for protein sequence for "
-            + sq.getName(),
+    assertTrue(
+            "No secondary structure assigned for protein sequence for "
+                    + sq.getName(),
             sq.getAnnotation() != null && sq.getAnnotation().length >= 1
                     && sq.getAnnotation()[0].hasIcons);
     assertTrue(
             "Secondary structure not associated for sequence "
-                    + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
+                    + sq.getName(),
+            sq.getAnnotation()[0].sequenceRef == sq);
   }
 
   /**
@@ -185,9 +195,9 @@ public class JmolParserTest
   public void testParse_missingResidues() throws Exception
   {
     PDBfile mctest = new PDBfile(false, false, false,
-            pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
+            pastePDBDataWithChainBreak, DataSourceType.PASTE);
     JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
-            AppletFormatAdapter.PASTE);
+            DataSourceType.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -208,9 +218,8 @@ public class JmolParserTest
   public void testParse_alternativeResidues() throws Exception
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
-            AppletFormatAdapter.PASTE);
-    JmolParser jtest = new JmolParser(pdbWithAltLoc,
-            AppletFormatAdapter.PASTE);
+            DataSourceType.PASTE);
+    JmolParser jtest = new JmolParser(pdbWithAltLoc, DataSourceType.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -252,24 +261,27 @@ public class JmolParserTest
   }
 
   @Test(groups = "Functional")
-  public void testLocalPDBId()
+  public void testLocalPDBId() throws Exception
   {
     JmolParser structureData;
-    try
-    {
-      structureData = new JmolParser("examples/DNMT1_MOUSE.pdb",
-              AppletFormatAdapter.FILE);
-      assertNotNull(structureData);
-      assertNotNull(structureData.getId());
-      assertEquals(structureData.getId(), "DNMT1_MOUSE.pdb");
-      assertNotNull(structureData.getSeqs());
-      assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
-      assertEquals(
-              structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
-              "dnmt1_mouse.pdb");
-    } catch (IOException e)
-    {
-      e.printStackTrace();
-    }
+    /*
+     * reads a local structure
+     */
+    structureData = new JmolParser("examples/testdata/localstruct.pdb",
+            DataSourceType.FILE);
+    assertNotNull(structureData);
+    /*
+     * local structure files should yield a false ID based on the filename
+     */
+    assertNotNull(structureData.getId());
+    assertEquals(structureData.getId(), "localstruct");
+    assertNotNull(structureData.getSeqs());
+    /*
+     * the ID is also the group for features derived from structure data 
+     */
+    String featureGroup = structureData.getSeqs().get(0)
+            .getSequenceFeatures().get(0).featureGroup;
+    assertNotNull(featureGroup);
+    assertEquals(featureGroup, "localstruct");
   }
 }